forked from hyperspy/hyperspy
/
test_eds_tem.py
564 lines (496 loc) · 22.3 KB
/
test_eds_tem.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HyperSpy is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HyperSpy. If not, see <http://www.gnu.org/licenses/>.
import numpy as np
import pytest
from hyperspy.components1d import Gaussian
from hyperspy.decorators import lazifyTestClass
from hyperspy.defaults_parser import preferences
from hyperspy.misc.eds import utils as utils_eds
from hyperspy.misc.test_utils import ignore_warning
from hyperspy.signals import EDSTEMSpectrum
@lazifyTestClass
class Test_metadata:
def setup_method(self, method):
# Create an empty spectrum
s = EDSTEMSpectrum(np.ones((4, 2, 1024)))
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time = 3.1
s.metadata.Acquisition_instrument.TEM.beam_energy = 15.0
self.signal = s
def test_sum_minimum_missing(self):
s = EDSTEMSpectrum(np.ones((4, 2, 1024)))
s.sum()
def test_sum_live_time1(self):
s = self.signal
old_metadata = s.metadata.deepcopy()
sSum = s.sum(0)
assert (
sSum.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time ==
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time * 2)
# Check that metadata is unchanged
print(old_metadata, s.metadata) # Capture for comparison on error
assert (old_metadata.as_dictionary() ==
s.metadata.as_dictionary()), "Source metadata changed"
def test_sum_live_time2(self):
s = self.signal
old_metadata = s.metadata.deepcopy()
sSum = s.sum((0, 1))
assert (
sSum.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time ==
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time
* 2 * 4)
# Check that metadata is unchanged
print(old_metadata, s.metadata) # Capture for comparison on error
assert (old_metadata.as_dictionary() ==
s.metadata.as_dictionary()), "Source metadata changed"
def test_sum_live_time_out_arg(self):
s = self.signal
sSum = s.sum(0)
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time = 4.2
s_resum = s.sum(0)
r = s.sum(0, out=sSum)
assert r is None
assert (
s_resum.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time ==
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time * 2)
np.testing.assert_allclose(s_resum.data, sSum.data)
def test_rebin_live_time(self):
s = self.signal
old_metadata = s.metadata.deepcopy()
dim = s.axes_manager.shape
s = s.rebin(new_shape=[dim[0] / 2, dim[1] / 2, dim[2]])
assert (
s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time ==
3.1 * 2 * 2)
# Check that metadata is unchanged
print(old_metadata, self.signal.metadata) # Captured on error
assert (old_metadata.as_dictionary() ==
self.signal.metadata.as_dictionary()), "Source metadata changed"
def test_offset_after_rebin(self):
s = self.signal
s.axes_manager[0].offset = 1
s.axes_manager[1].offset = 2
s.axes_manager[2].offset = 3
s2 = s.rebin(scale=(2, 2, 1))
assert s2.axes_manager[0].offset == 1.5
assert s2.axes_manager[1].offset == 2.5
assert s2.axes_manager[2].offset == s.axes_manager[2].offset
def test_add_elements(self):
s = self.signal
s.add_elements(['Al', 'Ni'])
assert s.metadata.Sample.elements == ['Al', 'Ni']
s.add_elements(['Al', 'Ni'])
assert s.metadata.Sample.elements == ['Al', 'Ni']
s.add_elements(["Fe", ])
assert s.metadata.Sample.elements == ['Al', "Fe", 'Ni']
s.set_elements(['Al', 'Ni'])
assert s.metadata.Sample.elements == ['Al', 'Ni']
def test_default_param(self):
s = self.signal
mp = s.metadata
assert (
mp.Acquisition_instrument.TEM.Detector.EDS.energy_resolution_MnKa ==
preferences.EDS.eds_mn_ka)
def test_TEM_to_SEM(self):
s = self.signal.inav[0, 0]
signal_type = 'EDS_SEM'
mp = s.metadata.Acquisition_instrument.TEM.Detector.EDS
mp.energy_resolution_MnKa = 125.3
sSEM = s.deepcopy()
sSEM.set_signal_type(signal_type)
mpSEM = sSEM.metadata.Acquisition_instrument.SEM.Detector.EDS
results = [
mp.energy_resolution_MnKa,
signal_type]
resultsSEM = [
mpSEM.energy_resolution_MnKa,
sSEM.metadata.Signal.signal_type]
assert results == resultsSEM
def test_get_calibration_from(self):
s = self.signal
scalib = EDSTEMSpectrum(np.ones(1024))
energy_axis = scalib.axes_manager.signal_axes[0]
energy_axis.scale = 0.01
energy_axis.offset = -0.10
s.get_calibration_from(scalib)
assert (s.axes_manager.signal_axes[0].scale ==
energy_axis.scale)
def test_are_microscope_parameters_missing(self):
assert not self.signal._are_microscope_parameters_missing()
del self.signal.metadata.Acquisition_instrument.TEM.beam_energy
del self.signal.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time
assert self.signal._are_microscope_parameters_missing()
@lazifyTestClass
class Test_quantification:
def setup_method(self, method):
s = EDSTEMSpectrum(np.ones([2, 2, 1024]))
energy_axis = s.axes_manager.signal_axes[0]
energy_axis.scale = 1e-2
energy_axis.units = 'keV'
energy_axis.name = "Energy"
s.set_microscope_parameters(beam_energy=200,
live_time=2.5, tilt_stage=0.0,
azimuth_angle=0, elevation_angle=35,
energy_resolution_MnKa=130,
beam_current=0.05)
elements = ['Al', 'Zn']
xray_lines = ['Al_Ka', 'Zn_Ka']
intensities = [300, 500]
for i, xray_line in enumerate(xray_lines):
gauss = Gaussian()
line_energy, FWHM = s._get_line_energy(xray_line, FWHM_MnKa='auto')
gauss.centre.value = line_energy
gauss.A.value = intensities[i]
gauss.sigma.value = FWHM
s.data[:] += gauss.function(energy_axis.axis)
s.set_elements(elements)
s.add_lines(xray_lines)
s.axes_manager[0].scale = 0.5
s.axes_manager[1].scale = 0.5
s.axes_manager[0].units = 'nm'
s.axes_manager[1].units = 'nm'
self.signal = s
def test_metadata(self):
TEM_md = self.signal.metadata.Acquisition_instrument.TEM
np.testing.assert_approx_equal(TEM_md.beam_energy, 200)
np.testing.assert_approx_equal(TEM_md.beam_current, 0.05)
np.testing.assert_approx_equal(TEM_md.Stage.tilt_alpha, 0.0)
np.testing.assert_approx_equal(TEM_md.Detector.EDS.live_time, 2.5)
np.testing.assert_approx_equal(TEM_md.Detector.EDS.elevation_angle, 35)
np.testing.assert_approx_equal(
TEM_md.Detector.EDS.energy_resolution_MnKa, 130)
self.signal.set_microscope_parameters(real_time=3.1)
self.signal.set_microscope_parameters(probe_area=1.2)
np.testing.assert_approx_equal(
TEM_md.probe_area, 1.2)
np.testing.assert_approx_equal(TEM_md.Detector.EDS.real_time, 3.1)
def test_quant_lorimer(self):
s = self.signal
method = 'CL'
kfactors = [1, 2.0009344042484134]
composition_units = 'weight'
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, kfactors,
composition_units)
s2 = s.rebin(new_shape=(1,1,1024)).squeeze().squeeze()
s2.quantification(intensities, method, kfactors,
composition_units, plot_result=True)
np.testing.assert_allclose(res[0].data, np.ones((2, 2)) * 22.70779,
atol=1e-3)
def test_quant_lorimer_warning(self):
s = self.signal
method = 'CL'
kfactors = [1, 2.0009344042484134]
composition_units = 'weight'
intensities = s.get_lines_intensity()
with pytest.raises(ValueError, match="Thickness is required for absorption"):
_ = s.quantification(intensities, method, kfactors,
composition_units,
absorption_correction=True,
thickness=None)
def test_quant_lorimer_ac(self):
s = self.signal
method = 'CL'
kfactors = [1, 2.0009344042484134]
composition_units = 'weight'
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, kfactors,
composition_units)
np.testing.assert_allclose(res[0].data, np.ones((2, 2)) * 22.70779,
atol=1e-3)
res2 = s.quantification(intensities, method, kfactors,
composition_units,
absorption_correction=True,
thickness=1.)
res3 = s.quantification(intensities, method, kfactors,
composition_units,
absorption_correction=True,
thickness=300.)
res4 = s.quantification(intensities, method, kfactors,
composition_units,
absorption_correction=True,
thickness=0.0001)
list.reverse(intensities)
list.reverse(kfactors)
res5 = s.quantification(intensities, method, kfactors,
composition_units,
absorption_correction=True,
thickness=300.)
np.testing.assert_allclose(res5[0][0].data, res3[0][1].data, atol=1e-5)
np.testing.assert_allclose(res2[0][0].data, np.ones((2, 2)) * 22.743013,
atol=1e-3)
np.testing.assert_allclose(res3[0][0].data, np.ones((2, 2)) * 31.816908,
atol=1e-3)
np.testing.assert_allclose(res[0].data, res4[0][0].data, atol=1e-5)
def test_quant_zeta(self):
s = self.signal
method = 'zeta'
composition_units = 'weight'
factors = [20, 50]
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, factors,
composition_units)
np.testing.assert_allclose(res[1].data, np.ones((2, 2)) * 2.7125736e-03,
atol=1e-3)
np.testing.assert_allclose(res[0][1].data,
np.ones((2, 2)) * 80.962287987, atol=1e-3)
res2 = s.quantification(intensities, method, factors,
composition_units,
absorption_correction=True,
thickness=1.)
res3 = s.quantification(intensities, method, factors,
composition_units,
absorption_correction=True,
thickness=100.)
assert res2 == res3
np.testing.assert_allclose(res2[0][1].data, np.ones((2, 2)) * 65.5867,
atol=1e-3)
def test_quant_cross_section_units(self):
s = self.signal.deepcopy()
s2 = self.signal.deepcopy()
s.axes_manager[0].units = 'µm'
s.axes_manager[1].units = 'µm'
s.axes_manager[0].scale = 0.5/1000
s.axes_manager[1].scale = 0.5/1000
method = 'cross_section'
factors = [3, 5]
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, factors)
res2 = s2.quantification(intensities, method, factors)
np.testing.assert_allclose(res[0][0].data, res2[0][0].data)
# Check that the quantification doesn't change the units of the signal
assert s.axes_manager[0].units == 'µm'
assert s.axes_manager[1].units == 'µm'
@pytest.mark.parametrize("axes", (None, "nav_axes", [0, 1], ['x', 'y']))
def test_get_probe_area(self, axes):
s = self.signal
s.axes_manager[0].name = 'x'
s.axes_manager[1].name = 'y'
s.axes_manager[0].units = 'µm'
s.axes_manager[1].units = 'µm'
s.axes_manager[0].scale = 0.5/1000
s.axes_manager[1].scale = 0.5/1000
if axes == "nav_axes":
axes = s.axes_manager.navigation_axes
np.testing.assert_allclose(s.get_probe_area(axes), 0.25, atol=1e-3)
@pytest.mark.parametrize("axes", (None, "nav_axes", [0], ['x']))
def test_get_probe_area_line_scan(self, axes):
s = self.signal.inav[0]
s.axes_manager[0].name = 'x'
s.axes_manager[0].units = 'µm'
s.axes_manager[0].scale = 0.5/1000
if axes == "nav_axes":
axes = s.axes_manager.navigation_axes
np.testing.assert_allclose(s.get_probe_area(axes), 0.25, atol=1e-3)
@pytest.mark.parametrize("axes", (None, "nav_axes", [0], ['x']))
def test_get_probe_area_line_scan_other_nav_axes(self, axes):
s = self.signal
s.axes_manager[0].name = 'x'
s.axes_manager[1].name = 'time'
s.axes_manager[0].units = 'µm'
s.axes_manager[1].units = 's'
s.axes_manager[0].scale = 0.5/1000
s.axes_manager[1].scale = 10
if axes == "nav_axes" or axes is None:
axes = s.axes_manager.navigation_axes
with pytest.raises(ValueError):
s.get_probe_area(axes)
else:
np.testing.assert_allclose(s.get_probe_area(axes), 0.25, atol=1e-3)
def test_zeta_vs_cross_section(self):
s = self.signal
factors = [3, 5]
method = 'zeta'
intensities = s.get_lines_intensity()
zfactors = utils_eds.edx_cross_section_to_zeta([3, 5], ['Al', 'Zn'])
factors2 = utils_eds.zeta_to_edx_cross_section(zfactors, ['Al', 'Zn'])
np.testing.assert_allclose(factors, factors2, atol=1e-3)
res = s.quantification(
intensities,
method,
factors = utils_eds.edx_cross_section_to_zeta([22.402, 21.7132],
['Al','Zn']))
res2 = s.quantification(intensities,
method='cross_section',
factors=[22.402, 21.7132])
np.testing.assert_allclose(res[0][0].data, res2[0][0].data, atol=1e-3)
np.testing.assert_allclose(res[0][0].data, np.ones((2, 2)) * 36.2969,
atol=1e-3)
def test_quant_cross_section(self):
s = self.signal
method = 'cross_section'
factors = [3, 5]
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, factors)
np.testing.assert_allclose(res[1][0].data, np.ones((2, 2)) * 21517.1647,
atol=1e-3)
np.testing.assert_allclose(res[1][1].data, np.ones((2, 2)) * 21961.6166,
atol=1e-3)
np.testing.assert_allclose(res[0][0].data, np.ones((2, 2)) * 49.4889,
atol=1e-3)
def test_method_error(self):
s = self.signal
method = 'random_method'
factors = [3, 5]
intensities = s.get_lines_intensity()
with pytest.raises(ValueError, match="Please specify method for quantification"):
_ = s.quantification(intensities, method, factors)
def test_quant_cross_section_ac(self):
s = self.signal
method = 'cross_section'
zfactors = [20, 50]
factors = utils_eds.zeta_to_edx_cross_section(zfactors, ['Al', 'Zn'])
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, factors,
absorption_correction=True)
res2 = s.quantification(intensities, method='zeta',
factors=zfactors,
absorption_correction=True)
np.testing.assert_allclose(res[0][1].data, np.ones((2, 2)) * 44.02534,
atol=1e-3)
np.testing.assert_allclose(res2[0][0].data, res[0][0].data, atol=1e-3)
def test_quant_zeros(self):
intens = np.array([[0.5, 0.5, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
[0.5, 0.0, 0.0]]).T
with ignore_warning(message="divide by zero encountered",
category=RuntimeWarning):
quant = utils_eds.quantification_cliff_lorimer(
intens, [1, 1, 3]).T
np.testing.assert_allclose(
quant,
np.array([[0.2, 0.2, 0.6],
[0.0, 0.25, 0.75],
[0.25, 0.0, 0.75],
[0.5, 0.5, 0.0],
[1.0, 0.0, 0.0]]))
def test_edx_cross_section_to_zeta(self):
cs = [3, 6]
elements = ['Pt', 'Ni']
res = utils_eds.edx_cross_section_to_zeta(cs, elements)
np.testing.assert_allclose(res, [1079.815272, 162.4378035], atol=1e-3)
def test_zeta_to_edx_cross_section(self):
factors = [1079.815272, 162.4378035]
elements = ['Pt', 'Ni']
res = utils_eds.zeta_to_edx_cross_section(factors, elements)
np.testing.assert_allclose(res, [3, 6], atol=1e-3)
def test_quant_element_order(self):
s = self.signal
s.set_elements([])
s.set_lines([])
lines = ['Zn_Ka', 'Al_Ka']
kfactors = [2.0009344042484134, 1]
intensities = s.get_lines_intensity(xray_lines=lines)
res = s.quantification(intensities, method='CL', factors=kfactors,
composition_units='weight')
assert res[0].metadata.Sample.xray_lines[0] == 'Zn_Ka'
assert res[1].metadata.Sample.xray_lines[0] == 'Al_Ka'
np.testing.assert_allclose(res[1].data, np.ones((2, 2)) * 22.70779,
atol=1e-3)
def test_CL_get_mass_thickness(self):
s = self.signal
method = 'CL'
kfactors = [1, 2.0009344042484134]
composition_units = 'weight'
intensities = s.get_lines_intensity()
res = s.quantification(intensities, method, kfactors,
composition_units)
mass_thickness = s.CL_get_mass_thickness(res, 100.)[0, 0]
np.testing.assert_allclose(mass_thickness, 6.1317741E-4)
thickness = np.array([[100., 90.0],
[85, 80.]])
mass_thickness2 = s.CL_get_mass_thickness(res, thickness)
np.testing.assert_allclose(mass_thickness2,
mass_thickness * thickness / 100)
@lazifyTestClass
class Test_vacum_mask:
def setup_method(self, method):
s = EDSTEMSpectrum(np.array([np.linspace(0.001, 0.5, 20)] * 100).T)
s.add_poissonian_noise()
self.signal = s
def test_vacuum_mask(self):
s = self.signal
assert s.vacuum_mask().data[0]
assert not s.vacuum_mask().data[-1]
@pytest.mark.parametrize('normalise_poissonian_noise', [True, False])
def test_decomposition(normalise_poissonian_noise):
s = EDSTEMSpectrum(np.ones(shape=(32, 32, 1024)))
s.add_poissonian_noise()
# default uses `vacuum_mask`
s.decomposition(normalise_poissonian_noise)
# test with numpy array mask
mask = s.vacuum_mask().data
s.decomposition(normalise_poissonian_noise, navigation_mask=mask)
@lazifyTestClass
class Test_simple_model:
def setup_method(self, method):
s = utils_eds.xray_lines_model(elements=['Al', 'Zn'],
weight_percents=[50, 50])
self.signal = s
def test_intensity(self):
s = self.signal
np.testing.assert_allclose(
[i.data[0] for i in s.get_lines_intensity(
integration_window_factor=5.0)],
[0.5, 0.5],
atol=1e-1)
def test_intensity_dtype_uint(self):
s = self.signal
s.data *= 1E5
s.change_dtype("uint")
bw = s.estimate_background_windows()
np.testing.assert_allclose(
[i.data[0] for i in s.get_lines_intensity(background_windows=bw)],
[5E4, 5E4],
rtol=0.03)
def test_with_signals_examples():
from hyperspy.misc.example_signals_loading import \
load_1D_EDS_TEM_spectrum as EDS_TEM_Spectrum
sig = EDS_TEM_Spectrum()
for s in (sig, sig.as_lazy()):
np.testing.assert_allclose(
np.array([res.data[0] for res in s.get_lines_intensity()]),
np.array([3710, 15872]))
class Test_eds_markers:
def setup_method(self, method):
s = utils_eds.xray_lines_model(elements=['Al', 'Zn'],
weight_percents=[50, 50])
self.signal = s
def test_plot_auto_add(self):
s = self.signal
s.plot(xray_lines=True)
# Should contain 6 lines
assert (
sorted(s._xray_markers.keys()) ==
['Al_Ka', 'Al_Kb', 'Zn_Ka', 'Zn_Kb', 'Zn_La', 'Zn_Lb1'])
def test_manual_add_line(self):
s = self.signal
s.add_xray_lines_markers(['Zn_La'])
assert (
list(s._xray_markers.keys()) ==
['Zn_La'])
assert len(s._xray_markers) == 1
# Check that the line has both a vertical line marker and text marker:
assert len(s._xray_markers['Zn_La']) == 2
def test_manual_remove_element(self):
s = self.signal
s.add_xray_lines_markers(['Zn_Ka', 'Zn_Kb', 'Zn_La'])
s.remove_xray_lines_markers(['Zn_Kb'])
assert (
sorted(s._xray_markers.keys()) ==
['Zn_Ka', 'Zn_La'])